Refactor docs/installation.md: update frontmatter metadata and restructure the installation guide. Broaden supported Python versions (3.10–3.12), clarify conda vs miniconda usage, add `uv` developer install instructions and editable `pip install -e` guidance, and reorganize sections for Conda, pip, Docker, GPU support, troubleshooting, and system/hardware considerations. Update TensorFlow deprecation timeline and GPU/CUDA guidance, improve admonitions/notes formatting, fix anchors/section refs, and add various wording and usability improvements.

Large cleanup and reorganization of docs/installation.md: rename heading, fix Markdown/admonition syntax, and normalize code fences. Clarified differences between Miniconda/Anaconda/conda, added a dedicated 'Build a conda environment' step, Windows-specific warnings, and tips for activating and managing environments. Added guidance for launching the GUI, created a simple conda env example, improved GPU/CUDA notes and troubleshooting links, and reformatted numerous paragraphs and images for readability.

Restructure and update the UseOverviewGuide page: fix markup (e.g. hint directive), add an Introduction and Workflow overview, embed/adjust images, and reorganize sections (What we support → Main modes; Additional learning resources; Usage advice & project types). Clarify installation reference, start/requirements guidance, and what you don't need. Add tips/warnings (recommend single-animal first, Windows admin warning), improve option headings for demos/GUI/terminal, and add brief terminal usage steps and useful links. Remove or comment out outdated/broken link references and tidy copy for clarity.

Rewrite and clarify installation guidance in docs/installation.md. Rephrase installation bullets (conda recommended, Docker note, GPU performance), fix image HTML closing and caption, and replace a single admonition with a tab-set providing CPU, NVIDIA GPU, and Apple M-chip GPU tabs (including CUDA/cuDNN guidance). Minor wording and link adjustments for clarity and reproducibility.

Refines wording and layout in the UseOverviewGuide: changes "What scenario" to "Which scenario", normalizes "Quick start" capitalization, and restructures multi-animal guidance into clearer bullet points. Expands guidance about using multianimal mode for single-animal projects (when a skeleton helps) and warns against treating fixed-position parts (e.g., whiskers) as separate individuals. Consolidates and repositions tutorial links, adds an important note to label identifiable animals consistently, updates the conversion link phrasing, and clarifies the Windows note to state admin is required for certain usage tasks (downloading models/symlinks) but not for installation.

Replace Markdown inline links with Sphinx {ref} cross-references, standardize admonition/class syntax, and clean up spacing and punctuation throughout docs/installation.md. Also normalize casing for the DeepLabCut heading, adjust image/code block indentation, add a MacOS GPU support footnote, and make minor clarity edits to GPU/PyTorch/TensorFlow installation notes and examples.

Clean up docs/installation.md: fix an escaped Windows activate path (activate.ps1), remove stray blank lines, and separate/version-check and update encouragement into their own paragraph. Add a "Data compatibility" subsection, rename the system-wide header to "System-wide installation considerations", and make small wording/formatting tweaks (e.g., emphasize "temporarily", reword potential package conflicts, and normalize "very slow"). These changes improve clarity and readability of the installation guide.

Adjust formatting in docs/UseOverviewGuide.md: indent fenced code blocks for proper rendering and normalize the ordered list numbering (use '1.' for sequential steps) for consistency in the instructions.

Disable references to the outdated 'installation tips' page in docs/installation.md. Replaced direct links and related guidance with HTML comments, added a note that the git-clone section is the place for editable installs, adjusted the pro-tip wording to point users to the test video, and commented out the 'Additional tips' block. Original content is preserved in comments for review.

Make minor copy edits to docs/gui/PROJECT_GUI.md for clarity: change "easy-entry point" to "easy entry point", replace "easy-to-deploy GUI interface" with "easy-to-use GUI interface", and rephrase the following sentence to more clearly state that several advanced features are not available in the Project GUI.

Refactor beginners-guide.md to center the guide on the DeepLabCut GUI. Updated the main heading and clarified startup wording (python -m deeplabcut) and project-creation workflow. Removed/replaced redundant installation text with a reference to the installation page and commented out an outdated course link. Added notes recommending the PyTorch engine, improved tips for video selection/copying, added guidance for defining bodyparts and multiple individuals, included a video tutorial GIF, and updated the next-steps reference to the GUI-specific manage-project page. Miscellaneous wording and screenshot tweaks for clarity.

Restructure and clarify the labeling documentation: reorganized headings and sections, consolidated frame selection guidance (automatic vs manual), and added an example workflow, important/tip admonitions, and a "Next steps" pointer to training/evaluation. Updated phrasing for clarity, fixed formatting (headings, links, and image reference), and replaced a quoted YAML note with unquoted text. These changes improve readability and better integrate the napari-DLC labeling workflow with the rest of the docs.

Revise the manage-project beginner guide to focus on editing the GUI configuration file. Renamed the section, added a file anchor, and reworded the intro to explain config.yaml as the central project record. Introduced a dedicated "Editing the configuration" and a step-by-step walkthrough that consolidates bodyparts and skeleton guidance (including details on entries/IDs), improved bullets and examples, and added a tip and an HTML comment. Updated the link to the labeling guide (file:labeling-gui) and made minor YAML/frontmatter and formatting fixes.

Revise docs/beginner-guides/Training-Evaluation.md: add RST anchor and restructure headings (Network training, Creating a training set, Starting the training process, Network evaluation, Next steps). Clarify wording (e.g. defaults described as “good” to start), convert tip to RST directive, adjust evaluation section formatting and images, and add reference to the video-analysis GUI section. Also change YAML notes value formatting.

Rework the beginner video-analysis doc to focus on the GUI workflow: add a file anchor, rename and restructure headings (Analyzing videos with your trained model, Generating labeled videos, Next steps), reorganize and clarify step-by-step instructions, and update copy. Also remove quoting from the frontmatter notes and add a TODO link comment for future cross-references.

Update several docs to improve formatting, clarity, and links. Convert inline notes to admonition blocks, fix spacing/indentation around images and note blocks, and bold example items for readability (docs/beginner-guides/beginners-guide.md). Clarify labeling guidance and emphasize labeling across multiple videos; update front-matter note to link to napari plugin docs (docs/beginner-guides/labeling.md). Adjust manage-project wording and next-step link to the labeling guide (docs/beginner-guides/manage-project.md). Add a brief napari usage recommendation with a link to the official napari docs (docs/gui/napari/basic_usage.md). These changes aim to make the GUI/napari workflow and labeling guidance clearer for beginners.

Polish docs/gui/PROJECT_GUI.md: rename headings for clarity ("Interactive Project Manager GUI" → "Project Manager GUI", "Get Started:" → "Getting started", "Video Demo" → "User guide" / "Video demos"); replace inline markdown links with Sphinx {ref} cross-references (napari and beginners guide); add an important note linking to the beginners guide and a tip to "Click on the images!". These changes improve consistency with the docs style and surface the step-by-step GUI guide.

Refactor docs/docker.md to improve formatting and clarify guidance. Renamed the section heading, convert several inline notes into MyST admonitions (important/note), wrap the napari-deeplabcut install guidance into an important block, and adjust the GPU reminder into an admonition. Minor rework of the mount/example instructions and commented out a redundant labelling note to reduce duplication and improve readability.

Simplify and update README text: streamline TensorFlow engine install instructions and add a planned deprecation target (tensorflow backend deprecated in v3.2). Replace prior dataset references with explicit Zenodo DOIs for SuperAnimal-Quadruped and SuperAnimal-TopViewMouse and add a citation to Ye et al. 2024. Clarify that models including AP-10K are available in the API/GUI, and fix minor wording in the funding acknowledgement ("following support").

Update docs/docker.md to improve clarity and accuracy of Docker guidance. Reworded introduction to explain that DeepLabCut images are available on DockerHub, that Docker requires a local Docker installation, and that containers provide a reproducible, isolated environment for terminal and Jupyter use. Explicitly state the DeepLabCut GUI is not supported in containers and move/strengthen the important note that the napari-deeplabcut plugin cannot be run inside Docker and must be installed locally (e.g. via pip). Clarified that deeplabcut-docker is a lightweight helper that will not disrupt local TensorFlow/PyTorch or other dependencies, and fixed wording/formatting issues.

Add brief guidance in the Training Dataset section to outline key steps (splitting labeled data and creating shuffle folders) so beginners have a clearer workflow before training. Also include a small formatting/whitespace adjustment in the GPU/Colab note.

Update docs/gui/napari/advanced_usage.md to improve clarity and usability. Reword the labeling progress note to emphasize that the displayed percentage is a rough estimate and that occluded/hidden keypoints are not counted. Expand and simplify instructions for jumping to a bodypart from the color scheme by breaking into explicit steps and clarifying behavior when the bodypart is already visible. Minor wording/formatting cleanups for readability.

Move the demo video link to appear before the warning block and tidy up minor whitespace/trailing-space issues in docs/gui/napari/basic_usage.md. These are formatting-only changes and do not alter substantive content.